The heme-sensitive regulator SbnI has a bifunctional role in staphyloferrin B production by Staphylococcus aureus

Abstract

Edited by F. Peter Guengerich Staphylococcus aureus infection relies on iron acquisition from its host. S. aureus takes up iron through heme uptake by the iron-responsive surface determinant (Isd) system and by the production of iron-scavenging siderophores. Staphyloferrin B (SB) is a siderophore produced by the 9-gene sbn gene cluster for SB biosynthesis and efflux. Recently, the ninth gene product, SbnI, was determined to be a free L-serine kinase that produces O-phospho-L-serine (OPS), a substrate for SB biosynthesis. Previous studies have also characterized SbnI as a DNA-binding regulatory protein that senses heme to control sbn gene expression for SB synthesis. Here, we present crystal structures at 1.9-2.1 Å resolution of a SbnI homolog from Staphylococcus pseudintermedius (SpSbnI) in both apo form and in complex with ADP, a product of the kinase reaction; the latter confirmed the active-site location. The structures revealed that SpSbnI forms a dimer through C-terminal domain swapping and a dimer of dimers through intermolecular disulfide formation. Heme binding had only a modest effect on SbnI enzymatic activity, suggesting that its two functions are independent and structurally distinct. We identified a heme-binding site and observed catalytic heme transfer between a heme-degrading protein of the Isd system, IsdI, and SbnI. These findings support the notion that SbnI has a bifunctional role contributing precursor OPS to SB synthesis and directly sensing heme to control expression of the sbn locus. We propose that heme transfer from IsdI to SbnI enables S. aureus to control iron source preference according to the sources available in the environment. Staphylococcus aureus is a prominent cause of infectious disease in humans (1, 2). Frequently associated with minor skin This work was supported by the Canadian Institutes of Health Research (CIHR) Grants MOP-49597 (to M. E. P. M.) and 374480 (to D. E. H.) and by the Natural Sciences and Engineering Research Council (NSERC) through Discovery Grant 0037-215 (to M. J. S.) and Postdoctoral Scholarships Doctoral (to M. M. V. and T. B. P.), and infrastructure support for structural biology was provided by the Canadian Foundation for Innovation (to M. E. P. M.). The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This article contains Figs. S1-S9 and Tables S1-S3. The atomic coordinates and structure factors (codes 5UJD and 6NR6) have been deposited in the Protein Data Bank (http://wwpdb.org/).

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“…Together with the fact that many Actinobacteria members possess a non-canonical heme biosynthesis pathway (Layer, 2021), these findings are suggestive of a rudimentary form of kin selection occurring in this lineage, based on hemetype compatibility. A similar observation in Staphylococcus aureus further substantiates this theory by showing that emergent subpopulations deficient in heme (DhemB) are more virulent when grown together with subpopulations deficient in menaquinone (DmenE), whereby both mutants reduce biosynthesis costs by exchanging the missing components with one another (Verstraete et al, 2019). The opposite, however, was true (e.g., DhemB mutants were less virulent) when grown in mixed culture with Enterococcus faecalis (Hammer et al, 2014), presumably due to differences in heme type.…”

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